When the Matoran arrived on Mata Nui, it served as Makuta's lair. Here he created the Kraata. He later put the Kraata in Energized Protodermis, transforming them into Rahkshi, assigned to find the Mask of Light, in which he was unsuccessful.

The Toa Mata face Teridax in the Mangaia

The only portal known to Mata Nui's villagers was the one directly beneath the Kini-Nui, which could only be opened once the Toa Mata had all acquired their Golden Kanohi. However, there was a second passage into the Mangaia, concealed underneath a giant, mysterious sundial located in the depths of Onu-Koro's Great Mine. Takua eventually opened the sundial by placing a gnomon in its center and shining a light so that the gnomon's shadow was at the 4 mark. When initially opened, though, all Ta-Matoran found in the small, crystalline chamber below was a hologram of a golden Hau hovering over a pedestal in the room's center.

Later, when the Toa Mata had finally collected all of their Great Kanohi, they met at the Great Temple, and descended into the Mangaia after acquiring their golden masks; while they were below, a small band of seven Matoran led by Takua protected the entrance above from being destroyed by Makuta's army of infected Rahi.

While below in the Mangaia, the Toa encountered the Manas, a uniquely vicious species of giant crab Rahi; these creatures were so powerful that eventually the Toa were forced to form the Toa Kaita, Akamai and Wairuha. After finally defeating the infected Rahi, the two Kaita proceeded into the very depths of Makuta's lair, only to be split back apart by Teridax's sheer destructive energy, and be forced to continue on foot.

During these events, the floating gold Kanohi within the sundial abruptly vanished, leading the Onu-Matoran to fear (correctly) that the sundial was actually another entrance into Teridax's lair. Fresh from the Battle of Kini-Nui, Takua returned to Onu-Koro, and found that a new passage way had opened up within. Activating it, Takua promptly descended into the pitch-black Mangaia to find the Toa. Eventually, he found the doorway to Makuta's inner sanctum, and witnessed the Toa's first battle with Makuta. After Teridax's supposed defeat, Takua ended up stumbling across the Bohrok Nests, right as Makuta was awakening the swarms. Pursued by a horde of Lehvak, Takua ultimately ended up stumbling across yet another passageway, this one leading from the lair and onto the beach of Ta-Wahi Beach, where he first began his journey.

A long time later, Takua, now known as Takanuva, returned to the Mangaia via the now-shattered Kini-Nui entrance to confront Makuta once and for all. After winning a deadly version of Kolhii against Makuta, he and Teridax ended up falling into the pool of energized protodermis, fusing them into Takutanuva. Takutanuva then lifted the gate to Metru Nui, and he held it up while all of Mata Nui's inhabitants crossed through, stopping only to bring Jaller back to life. Weakened after the revival, the door crushed Takutanuva, destroying Teridax's armor.

A few days later, a band of six ex-Dark Hunters known as the Piraka stumbled across the Mangaia. The Spear of Fusion was discovered, and Hakann's inadvertent mishandling of the Spear caused it to strike Vezok and divide him into two separate beings: himself, and the half-mad Vezon, who became the seventh Piraka.

The Order of Mata Nui later destroyed the Energized Protodermis in Mangaia.

Mangaia was possibly later destroyed by the awakening of Mata Nui (with Teridax's mind) after "Toa" Ignika sacrificed his life for the Universe.